# Pairwise INTegration of functional genomics data

## Documentation for package ‘pint’ version 1.28.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

as.data.frame-method | Class "ChromosomeModels"
as.data.frame-method | Class "GenomeModels"
ChromosomeModels-class | Class "ChromosomeModels"
dependency score plotting | Dependency score plotting
findModel | Class "ChromosomeModels"
findModel-method | Class "ChromosomeModels"
findModel-method | Class "GenomeModels"
fit.byname | Fit dependency model around one gene between two data sets.
fit.cgh.mir.byname | Fit dependency model around one gene between two data sets.
fit.cgh.mrna.byname | Fit dependency model around one gene between two data sets.
fixed.window | Form data with a selected window size for the model fitting
geneCopyNum | Gene copy number data in chromosome 17
GeneDependencyModel-class | Class "GeneDependencyModel"
geneExp | Gene expression data in chromosome 17
GenomeModels-class | Class "GenomeModels"
get.neighboring.probes | Get neighboring probes
get.neighs | get.neighs
getArm | Class "ChromosomeModels"
getArm-method | Class "ChromosomeModels"
getArm-method | Class "GeneDependencyModel"
getChromosome | Class "ChromosomeModels"
getChromosome-method | Class "ChromosomeModels"
getChromosome-method | Class "GeneDependencyModel"
getGeneName | Class "ChromosomeModels"
getGeneName-method | Class "ChromosomeModels"
getGeneName-method | Class "GeneDependencyModel"
getLoc | Class "GeneDependencyModel"
getLoc-method | Class "ChromosomeModels"
getLoc-method | Class "GeneDependencyModel"
getModelMethod | Class "ChromosomeModels"
getModelMethod-method | Class "ChromosomeModels"
getModelMethod-method | Class "GenomeModels"
getModelNumbers | Class "ChromosomeModels"
getModelNumbers-method | Class "ChromosomeModels"
getModelNumbers-method | Class "GenomeModels"
getParams | Class "ChromosomeModels"
getParams-method | Class "ChromosomeModels"
getParams-method | Class "GenomeModels"
getPArm | Class "ChromosomeModels"
getPArm-method | Class "ChromosomeModels"
getQArm | Class "ChromosomeModels"
getQArm-method | Class "ChromosomeModels"
getScore | Class "GeneDependencyModel"
getScore-method | Class "ChromosomeModels"
getScore-method | Class "GeneDependencyModel"
getWindowSize | Class "ChromosomeModels"
getWindowSize-method | Class "ChromosomeModels"
getWindowSize-method | Class "GeneDependencyModel"
getWindowSize-method | Class "GenomeModels"
getZ-method | Class "GeneDependencyModel"
isEmpty | Class "ChromosomeModels"
isEmpty-method | Class "ChromosomeModels"
iterative.window | Form data with a selected window size for the model fitting
join.top.regions | Merge the overlapping top chromosomal regions.
order.feature.info | Order the gene information table by chromosomal locations.
orderGenes | Class "ChromosomeModels"
orderGenes-method | Class "ChromosomeModels"
orderGenes-method | Class "GenomeModels"
pint.data | Forms a data set and pairs samples in two data sets.
pint.match | Forms a data set and pairs samples in two data sets.
plot.ChromosomeModels | Dependency score plotting
plot.GeneDependencyModel | Dependency score plotting
plot.GenomeModels | Dependency score plotting
screen.cgh.mir | Fits dependency models to chromosomal arm, chromosome or the whole genome.
screen.cgh.mrna | Fits dependency models to chromosomal arm, chromosome or the whole genome.
setArm<- | Class "GeneDependencyModel"
setArm<--method | Class "GeneDependencyModel"
setChromosome<- | Class "GeneDependencyModel"
setChromosome<--method | Class "GeneDependencyModel"
setGeneName<- | Class "GeneDependencyModel"
setGeneName<--method | Class "GeneDependencyModel"
setLoc<- | Class "GeneDependencyModel"
setLoc<--method | Class "GeneDependencyModel"
sparse.window | Form data with a selected window size for the model fitting
summarize.region.parameters | Summarize overlapping models.
topGenes | Class "ChromosomeModels"
topGenes-method | Class "ChromosomeModels"
topGenes-method | Class "GenomeModels"
topModels | Class "ChromosomeModels"
topModels-method | Class "ChromosomeModels"
topModels-method | Class "GenomeModels"
W.effects | The model parameters z and W
z.effects | The model parameters z and W
[[ | Class "ChromosomeModels"
[[-method | Class "ChromosomeModels"
[[-method | Class "GenomeModels"
[[<- | Class "ChromosomeModels"
[[<--method | Class "ChromosomeModels"
[[<--method | Class "GenomeModels"